Title: Employing the gut microbiome to accelerate effective initiation of rheumatoid arthritis therapy ABSTRACT Rheumatoid arthritis (RA) is a complex, multifactorial, autoimmune disorder that affects ~1% of the worldwide population (~2 million adults in the US alone). It is characterized by chronic synovitis that, when left untreated, can result in irreversible joint destruction and deformity, leading to increased morbidity and all-cause mortality. The last three decades have witnessed impressive advances in the understanding of disease pathogenesis and therapeutic outcomes. In fact, the use of methotrexate first, and the subsequent incorporation of anti-TNF (TNFi) and other ?biologics? have led to substantial improvements in RA clinical outcomes, enhancing the quality of life for millions of patients with inflammatory arthritis. Despite this progress, however, a significant question still remains unanswered: why do over 50% of RA patients with moderate to severe arthritis fail to respond appropriately to these agents? Pharmacomicrobiomics ? an emerging field of study that investigates the effect of variations within the human gut microbiome on drugs ? promises to overcome these barriers and facilitate precision medicine approaches in autoimmune disease. Methotrexate (MTX), a dihydrofolate (DHF) reductase inhibitor, remains the anchor drug for the treatment of RA and is used widely throughout the world. While quite effective, oral MTX achieves significant results in less than 50% of patients and remission in only a quarter of them. It is well established that the inter-individual bioavailability of MTX is extremely variable, ranging from 10 to 80%. The reasons for this are presumably multifactorial. However, the intestinal microbiome and its enzymatic machinery are likely to play a significant role, based on our Preliminary Results and given that animals treated with antibiotics or kept under germ-free conditions show significant differences in MTX metabolism relative to control animals. Our multidisciplinary team composed of rheumatologists, bioinformaticians, pharmacologists and microbiome researchers will address our overarching goal to study: a) if baseline intestinal microbiome, its genes, and associated metabolites can be used to predict the immunomodulatory responses to MTX in treatment-nave, new-onset RA (NORA) patients; and b) if the gut microbiomes of MTX non-responders can be manipulated to modulate MTX metabolism and bioavailability. We believe that the results of our highly translational, innovative studies will directly influence therapeutic approaches for the treatment of RA and offer a more personalized approach in which the clinical efficacy response would be predicted early (and potentially improved by microbiome-targeted adjuvant therapies) in any given patient about to initiate MTX, limiting or preventing disease progression and ultimately avoiding wasteful health expenditures (estimated as ~$50,000/year/patient in direct costs). Importantly, we anticipate that our studies will establish generalizable approaches in rheumatology and autoimmunity that could be more broadly applied to the study and clinical maximization of other similar small molecules (e.g., JAK inhibitors) or even biologic agents (e.g., anti-TNF mAbs).